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Among 2,186 U.S. adults with invasive cancer and laboratory-confirmed SARS-CoV-2 infection, we examined the association of COVID-19 treatments with 30-day all-cause mortality and factors associated with treatment. Logistic regression with multiple adjustments (e.g., comorbidities, cancer status, baseline COVID-19 severity) was performed. Hydroxychloroquine with any other drug was associated with increased mortality versus treatment with any COVID-19 treatment other than hydroxychloroquine or untreated controls; this association was not present with hydroxychloroquine alone. Remdesivir had numerically reduced mortality versus untreated controls that did not reach statistical significance. Baseline COVID-19 severity was strongly associated with receipt of any treatment. Black patients were approximately half as likely to receive remdesivir as white patients. Although observational studies can be limited by potential unmeasured confounding, our findings add to the emerging understanding of patterns of care for patients with cancer and COVID-19 and support evaluation of emerging treatments through inclusive prospective controlled trials.Significance:Evaluating the potential role of COVID-19 treatments in patients with cancer in a large observational study, there was no statistically significant 30-day all-cause mortality benefit with hydroxychloroquine or high-dose corticosteroids alone or in combination; remdesivir showed potential benefit. Treatment receipt reflects clinical decision-making and suggests disparities in medication access.This article is highlighted in the In This Issue feature, p. 1426

Supplemental tables, figures, and list of participants

Molecular profiling studies have enabled discoveries for metastatic prostate cancer (MPC) but have predominantly occurred in academic medical institutions and involved non-representative patient populations. We established the Metastatic Prostate Cancer Project (MPCproject, mpcproject.org), a patient-partnered initiative to involve patients with MPC living anywhere in the US and Canada in molecular research. Here, we present results from our partnership with the first 706 MPCproject participants. While 41% of patient partners live in rural, physician-shortage, or medically underserved areas, the MPCproject has not yet achieved racial diversity, a disparity that demands new initiatives detailed herein. Among molecular data from 333 patient partners (572 samples), exome sequencing of 63 tumor and 19 cell-free DNA (cfDNA) samples recapitulated known findings in MPC, while inexpensive ultra-low-coverage sequencing of 318 cfDNA samples revealed clinically relevant

Background: Angiosarcoma (ASC) represents 1-2% of soft tissue sarcomas. Due to its rarity, to date, no large-scale studies have been done to systematically identify ASC-predisposition genes and the broader landscape of pathogenic germline variants in patients with ASC remains unclear. Methods: Through the Angiosarcoma Project, an ongoing patient-partnered research approach that allows patients living anywhere in the U.S. or Canada with angiosarcoma to participate through a website, blood and saliva samples were collected from more than 300 patients and whole-exome-sequencing was performed. Machine-learning frameworks were used to identify germline short variants (SNPs, indels) and rare germline copy number variants (CNVs). The pathogenicity of variants in 107 curated cancer-predisposition and sarcoma-related genes were evaluated according to the ACMG guidelines. A short-variant-based gene-burden analysis was then performed using 223 unrelated ASC patients and 4557 ancestry-matched unrelated cancer-free controls. Results: In total, 38 patients (17.04%) carried at least one pathogenic short variant, including 37 carrying germline heterozygous pathogenic variants in POT1 (9, 4.04%), BRCA2 (3, 1.35%), CHEK2 (3, 1.35%), MUTYH (3, 1.35%), BRCA1 (2, 0.90%), PRF1 (2, 0.90%), ERCC3 (1, 0.45%), TP53 (2, 0.90%), ATM (1, 0.45%), TSHR (1, 0.45%), TSC2 (1, 0.45%), SDHA (1, 0.45%), SBDS (1, 0.45%), MSH6 (1, 0.45%), MITF (1, 0.45%), MET (1, 0.45%), LZTR1 (1, 0.45%), FH (1, 0.45%), ERCC2 (1, 0.45%), XPC (1, 0.45%). In addition, one patient harbored pathogenic short variants in both BRCA1 and ERCC3. In the 8 unique CNVs detected in 10 (4.55%) patients, 6 were classified as pathogenic including 3 heterozygous duplications overlapping MSH2, LZTR1, SMARCB1, and 3 heterozygous deletions overlapping NF1, MSH2, and WRN. Two unique heterozygous duplications met VUS criteria including one overlapping ERCC2 and one overlapping SMARCB1. In a comparison between ASC patients and cancer-free controls of predominantly European ancestry, we found ASC patients tobe 40 times more likely to carry a pathogenic variant in POT1 (OR: 42.91, CI: [15.40-174.08], q < 0.001, p < 0.001), while TP53 was nominally significant (OR: 7.37, CI: [1.19 - 41.13], p = 0.037). Conclusion: We confirmed prior observations of POT1 being responsible for ASC and called for attention to investigate the effect of germline CNVs in ASC. Overall, the elucidation of various germline elements associated with ASC risk highlighted the value and importance of patient-partnered research, particularly for rare cancers, and the analysis support using germline testing of patients for more precise clinical management. Citation Format: Hoyin Chu, Marissa Hollyer, Seunghun Han, Sabrina Y. Camp, Riaz Gillani, Eliezer Van Allen, Nikhil Wagle, Corrie A. Painter, Saud H. AlDubayan. Patient-partnered research enables germline characterization of angiosarcoma predisposition genes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6064.

Introduction: Hospitalized patients with COVID-19 may have increased risk of venous thromboembolism (VTE) and pulmonary embolism (PE). Cancer and anti-cancer therapies are well-known additional risk factors for VTE. Nonetheless, the VTE risk in patients with both cancer and COVID-19 infection remains unknown as recent studies have not found an association due to sample size limitations. We report the incidence of and risk factors for VTE and PE among hospitalized patients with cancer and COVID-19. Methods: The COVID-19 and Cancer Consortium (CCC19) developed an international retrospective cohort study (NCT04354701) to investigate the clinical course and complications of COVID-19 among adult patients with an active or previous history of cancer. For the current study, cumulative incidences of clinically detected VTE and PE were analyzed among hospitalized patients with laboratory confirmed SARS-CoV-2. Pre-specified subgroup analysis was performed to examine the interaction between intensive care unit (ICU) admission and recent anti-cancer therapy on VTE outcomes. Bivariable logistic regression analyses were conducted to assess the association between baseline variables and VTE; unadjusted odds ratios (OR) and 95% confidence interval (CI) were reported. These variables included age, sex, obesity (BMI>30), race/ethnicity, performance status, comorbidities, blood type, history of VTE, recent surgery, recent anti-cancer therapy, cancer subtype VTE risk grouping (adapted from Khorana Score), pre-admission anticoagulant or antiplatelet use, and ICU admission status. Results: From March 17, 2020 to July 31, 2020, 3914 patients were enrolled in the CCC19 registry. For the present analysis, patients were excluded if they had inadequate follow-up The overall incidence of inhospital VTE and PE was 9.3% and 5.2%, respectively. The corresponding estimates were 13.4% and 7.9% among the ICU subgroup. On bivariable analysis, significant predictors of VTE included ICU admission, recent anti-cancer therapy, active cancer status, cancer subtype VTE risk grouping, and pre-admission antiplatelet use (Table 1). Pre-admission anticoagulant use had significant associations with PE but not VTE. Multivariable adjustment is ongoing to identify independent risk factor for VTE and clarify the impact of pre-admission anticoagulant/antiplatelet use controlled for other potential confounders. Both ICU admission status and anti-cancer therapy increased the risk of VTE independently. Non-ICU patients not on anti-cancer therapy had the lowest incidence of VTE (4.5%), whose estimate was similar to that reported in the non-cancer hospitalized population with COVID-19 infection. Patients with either ICU admission or recent anti-cancer therapy had the intermediate risk (11.0%), whereas ICU patients with recent anti-cancer therapy had the highest risk (16.7%). We did not observe confounding or effect modification by the ICU subgroup on the association between anti-cancer therapy and VTE. Conclusion: In this cohort study of hospitalized patients with cancer and COVID-19, recent anti-cancer therapy, active disease, high-risk VTE cancer subtypes, and ICU admission have increased risk of VTE and PE, while pre-admission anticoagulant/antiplatelet therapy may reduce the risk. This information will aid in developing a risk prediction tool for VTE in hospitalized patients with cancer and COVID-19. Disclosures Kuderer: G1 Therapeutics: Consultancy; Total Health: Consultancy; Invitae: Consultancy; Beyond Springs: Consultancy; Bristol-Myers Squibb: Consultancy; celldex: Consultancy; Bayer: Consultancy; Spectrum Pharmaceuticals: Consultancy; Janssen: Consultancy. Warner:HemOnc.orgLLC: Other: Shareholder/Stockholder/Stock options; IBM Watson Health: Consultancy; Westat: Consultancy; National Cancer Institute: Research Funding. Shah:American Cancer Society and the Hope Foundation for Cancer Research: Research Funding; National Cancer Institute: Research Funding. Zon:Amagma Therapeutics.: Consultancy, Other: stockholder. Shah:Aspen Pharma: Research Funding. Gulati:Puma Biotechnology: Consultancy; AstraZeneca: Research Funding; Isoray: Research Funding. Khaki:Merck: Other: share/stockholder; Pfizer: Other: share/stockholder. Thompson:AIM Specialty Health, BMS, GlaxoSmithKline, Takeda, Via Oncology: Membership on an entity's Board of Directors or advisory committees; Synapse Precision Medical Council: Other: Travel expenses; Doximity: Current equity holder in publicly-traded company, Membership on an entity's Board of Directors or advisory committees. Grivas:Oncogenex: Research Funding; Immunomedics: Research Funding; Debiopharm: Research Funding; Bavarian Nordic,: Research Funding; QED Therapeutics: Honoraria; Seattle Genetics: Honoraria; Roche: Honoraria; Pfizer: Honoraria, Research Funding; Mirati Therapeutics: Honoraria, Research Funding; Merck: Honoraria, Research Funding; Janssen: Honoraria; Heron Therapeutics: Honoraria; GlaxoSmithKline: Honoraria; Genzyme: Honoraria; Genentech: Honoraria, Research Funding; Foundation Medicine: Honoraria; Exelixis: Honoraria; EMD Serono: Honoraria; Driver: Honoraria; Clovis Oncology: Honoraria, Research Funding; Bristol-Myers Squibb,: Consultancy, Honoraria, Research Funding, Speakers Bureau; Biocept: Honoraria; Bayer: Honoraria, Research Funding; Astra Zeneca: Honoraria, Research Funding. de Lima Lopes:Bavarian Nordic: Research Funding; NOVARTIS: Research Funding; Tesaro: Research Funding; GSK: Research Funding; G1 Therapeutics: Research Funding; adaptimmune: Research Funding; BMS: Research Funding; Lilly: Research Funding; Merck Sharp & Dohme: Research Funding; Astra Zeneca: Consultancy, Research Funding; Pfizer: Consultancy, Research Funding; Boehringer Ingelheim: Honoraria; Janssen: Research Funding; rgenix: Research Funding; Blueprint Medicines: Research Funding; Genentech: Research Funding; Roche: Research Funding; EMD Serono: Research Funding. Shyr:Roche: Consultancy; Novartis: Consultancy; Pfizer: Consultancy; Johnson & Johnson: Consultancy; GlaxoSmithKline: Consultancy; AstraZeneca: Consultancy, Speakers Bureau; Boehringer Ingelheim: Speakers Bureau; Eisai: Speakers Bureau. Pennell:Merck: Consultancy; Cota: Consultancy; Inivata: Consultancy; G1 Therapeutics: Consultancy; Astrazeneca: Consultancy; BMS: Consultancy; Eli Lilly: Consultancy; Amgen: Consultancy; Genentech: Consultancy. Friese:Eli Lilly: Consultancy; Patient-Centered Outcomes Research Institute: Membership on an entity's Board of Directors or advisory committees; Agency for Healthcare Research and Quality: Research Funding; National Cancer Institute: Research Funding; Merck Foundation: Research Funding; National Comprehensive Cancer Network: Research Funding; Pfizer: Research Funding; Eli Lilly: Consultancy. Patel:reast Cancer Research Foundation: Research Funding; Sanofi: Research Funding; Odonate Therapeutics: Research Funding; Radius: Honoraria; Genentech: Research Funding. Halmos:Foundation Medicine: Consultancy, Research Funding; Amgen: Consultancy, Research Funding; Guardant Health: Consultancy, Research Funding; Novartis: Consultancy, Research Funding; Boehringer-Ingelheim: Consultancy, Research Funding; Merck: Consultancy, Research Funding; Bristol-Myers Squibb: Consultancy, Research Funding; AstraZeneca: Consultancy, Research Funding; Pfizer: Consultancy, Research Funding; Eli-Lilly: Research Funding; Advaxis: Research Funding; Mirati: Research Funding; Takeda: Research Funding; GSK: Research Funding; AbbVie: Research Funding; Genentech: Consultancy; TPT: Consultancy. Choueiri:Pfizer: Consultancy, Honoraria, Research Funding; Pionyr: Consultancy, Other; Merck: Consultancy, Honoraria, Research Funding; Roche Products Limited: Honoraria, Research Funding; Roche: Consultancy, Honoraria, Research Funding; F. Hoffmann-La Roche: Honoraria, Research Funding; GlaxoSmithKline: Consultancy, Honoraria, Research Funding; Lilly: Consultancy, Research Funding; Peloton: Consultancy, Honoraria, Research Funding; Novartis: Consultancy, Honoraria, Research Funding; Tempest: Consultancy, Other; Lilly Ventures: Consultancy; International Patent Application No. PCT/US2018/12209, entitled "PBRM1 Biomarkers Predictive of Anti-Immune Checkpoint Response," filed January 3, 2018, claiming priority to U.S. Provisional Patent Application No. 62/445,094, filed January 11, 2017: Patents & Royalties; Prometheus Labs: Consultancy, Honoraria, Research Funding; Corvus: Consultancy, Honoraria, Research Funding; AstraZeneca: Consultancy, Honoraria, Research Funding; Alexion: Consultancy, Honoraria, Research Funding; Bayer: Consultancy, Honoraria, Research Funding; Bristol Myers-Squibb/ER Squibb and sons LLC: Consultancy, Honoraria, Research Funding; Cerulean: Consultancy, Honoraria, Research Funding; Eisai: Consultancy, Honoraria, Research Funding; oundation Medicine Inc.: Consultancy, Honoraria, Research Funding; International Patent Application No. PCT/US2018/058430, entitled "Biomarkers of Clinical Response and Benefit to Immune Checkpoint Inhibitor Therapy," filed October 31, 2018, claiming priority to U.S. Provisional Patent Application No. 62/581,175, filed N: Patents & Royalties; Calithera: Research Funding; Analysis Group: Research Funding; Sanofi/Aventis: Consultancy, Honoraria, Research Funding; Takeda: Research Funding; EMD Serono: Consultancy, Honoraria; Up-to-Date: Consultancy, Honoraria; NCCN: Consultancy, Honoraria; Lilly Oncology: Consultancy, Honoraria; Heron Therapeutics: Consultancy, Honoraria; Lancet Oncology: Honoraria; NEJM: Honoraria; American Society of Medical Oncology: Honoraria; Harborside Press: Honoraria; Navinata Healthcare: Honoraria; Platform Q: Honoraria; L-path, Kidney Cancer Journal, Clinical Care Options: Honoraria; Research to Practice: Honoraria; PeerView and PER: Honoraria; OnClive: Honoraria; Genentech: Consultancy, Honoraria, Research Funding; Ipsen: Consultancy, Honoraria, Research Funding; Tracon: Research Funding; Exelixis: Consultancy, Honoraria, Research Funding; Analysis Group: Consultancy, Honoraria; Michael J. Hennessy (MJH) Associates, Inc: Honoraria. Peters:Debiopharm: Consultancy, Honoraria; Bristol-Myers Squibb: Consultancy, Honoraria, Research Funding; Boehringer-Ingelheim: Consultancy, Honoraria; Blueprint Medicines: Consultancy, Honoraria; Bioinvent: Consultancy, Honoraria; Biocartis: Consultancy, Honoraria; Eli Lilly: Consultancy, Honoraria; F. Hoffmann-La Roche: Consultancy, Honoraria, Research Funding; Foundation Medicine: Consultancy, Honoraria; Illumina: Consultancy, Honoraria, Research Funding; Janssen: Consultancy, Honoraria; Merck Sharp and Dohme: Consultancy, Honoraria, Research Funding; Merck Serono: Consultancy, Honoraria, Research Funding; Merrimack: Consultancy, Honoraria; Novartis: Consultancy, Honoraria, Research Funding; Pharma Mar: Consultancy, Honoraria; Pfizer: Consultancy, Honoraria, Research Funding; Regeneron: Consultancy, Honoraria; Sanofi: Consultancy, Honoraria; Seattle Genetics: Consultancy, Honoraria; Takeda: Consultancy, Honoraria; Vaccibody: Consultancy, Honoraria; Biodesix: Research Funding; Daiichi Sankyo: Consultancy, Honoraria; Clovis: Consultancy, Honoraria, Research Funding; Bayer: Consultancy, Honoraria; AstraZeneca: Consultancy, Honoraria, Research Funding; Abbvie: Consultancy, Honoraria; Amgen: Consultancy, Honoraria, Research Funding. Painter:Roche: Other: stock or other ownership; OPKO Health Inc: Other: stock or other ownership; Inovio: Other: stock or other ownership; Epizyme: Other: stock or other ownership; Pfizer: Other: stock or other ownership. Rini:Astra-Zeneca: Research Funding; PTC Therapeutics: Other: Sotckholder/stock options; Surface Oncology: Consultancy; Synthorx: Consultancy; 3D Medicine: Consultancy; Arravive: Consultancy; Bristol-Myers Squibb: Consultancy, Research Funding; AVEO: Consultancy, Research Funding; Pfizer: Consultancy, Research Funding; Roche: Consultancy, Research Funding; Merck: Consultancy, Research Funding. Lyman:Amgen: Research Funding; Mylan: Consultancy; Beyond Spring: Consultancy; Samsung: Consultancy; Sandoz: Consultancy; Invitae: Consultancy; Spectrum: Consultancy; G1 Therapeutics: Consultancy. Connors:Bristol-Myers Squibb: Consultancy, Honoraria; Portola: Honoraria; CSL Behring: Research Funding; Takeda: Honoraria; Abbott: Consultancy, Honoraria. Rosovsky:Bristol-Myers Squibb: Consultancy, Research Funding; Janssen: Consultancy, Research Funding; Dova: Consultancy; Portola: Consultancy.

In a large observational study in patients with COVID-19 and cancer, survival was not significantly influenced by receipt of COVID-19 treatments, except hydroxychloroquine plus any other treatment, which was associated with reduced survival., Among 2,186 U.S. adults with invasive cancer and laboratory-confirmed SARS-CoV-2 infection, we examined the association of COVID-19 treatments with 30-day all-cause mortality and factors associated with treatment. Logistic regression with multiple adjustments (e.g., comorbidities, cancer status, baseline COVID-19 severity) was performed. Hydroxychloroquine with any other drug was associated with increased mortality versus treatment with any COVID-19 treatment other than hydroxychloroquine or untreated controls; this association was not present with hydroxychloroquine alone. Remdesivir had numerically reduced mortality versus untreated controls that did not reach statistical significance. Baseline COVID-19 severity was strongly associated with receipt of any treatment. Black patients were approximately half as likely to receive remdesivir as white patients. Although observational studies can be limited by potential unmeasured confounding, our findings add to the emerging understanding of patterns of care for patients with cancer and COVID-19 and support evaluation of emerging treatments through inclusive prospective controlled trials. Significance: Evaluating the potential role of COVID-19 treatments in patients with cancer in a large observational study, there was no statistically significant 30-day all-cause mortality benefit with hydroxychloroquine or high-dose corticosteroids alone or in combination; remdesivir showed potential benefit. Treatment receipt reflects clinical decision-making and suggests disparities in medication access. This article is highlighted in the In This Issue feature, p. 1426

Summary Background Data on patients with COVID-19 who have cancer are lacking. Here we characterise the outcomes of a cohort of patients with cancer and COVID-19 and identify potential prognostic factors for mortality and severe illness. Methods In this cohort study, we collected de-identified data on patients with active or previous malignancy, aged 18 years and older, with confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection from the USA, Canada, and Spain from the COVID-19 and Cancer Consortium (CCC19) database for whom baseline data were added between March 17 and April 16, 2020. We collected data on baseline clinical conditions, medications, cancer diagnosis and treatment, and COVID-19 disease course. The primary endpoint was all-cause mortality within 30 days of diagnosis of COVID-19. We assessed the association between the outcome and potential prognostic variables using logistic regression analyses, partially adjusted for age, sex, smoking status, and obesity. This study is registered with ClinicalTrials.gov, NCT04354701, and is ongoing. Findings Of 1035 records entered into the CCC19 database during the study period, 928 patients met inclusion criteria for our analysis. Median age was 66 years (IQR 57–76), 279 (30%) were aged 75 years or older, and 468 (50%) patients were male. The most prevalent malignancies were breast (191 [21%]) and prostate (152 [16%]). 366 (39%) patients were on active anticancer treatment, and 396 (43%) had active (measurable) cancer. At analysis (May 7, 2020), 121 (13%) patients had died. In logistic regression analysis, independent factors associated with increased 30-day mortality, after partial adjustment, were: increased age (per 10 years; partially adjusted odds ratio 1·84, 95% CI 1·53–2·21), male sex (1·63, 1·07–2·48), smoking status (former smoker vs never smoked: 1·60, 1·03–2·47), number of comorbidities (two vs none: 4·50, 1·33–15·28), Eastern Cooperative Oncology Group performance status of 2 or higher (status of 2 vs 0 or 1: 3·89, 2·11–7·18), active cancer (progressing vs remission: 5·20, 2·77–9·77), and receipt of azithromycin plus hydroxychloroquine (vs treatment with neither: 2·93, 1·79–4·79; confounding by indication cannot be excluded). Compared with residence in the US-Northeast, residence in Canada (0·24, 0·07–0·84) or the US-Midwest (0·50, 0·28–0·90) were associated with decreased 30-day all-cause mortality. Race and ethnicity, obesity status, cancer type, type of anticancer therapy, and recent surgery were not associated with mortality. Interpretation Among patients with cancer and COVID-19, 30-day all-cause mortality was high and associated with general risk factors and risk factors unique to patients with cancer. Longer follow-up is needed to better understand the effect of COVID-19 on outcomes in patients with cancer, including the ability to continue specific cancer treatments. Funding American Cancer Society, National Institutes of Health, and Hope Foundation for Cancer Research.

Despite rare cancers accounting for 25% of adult tumors1, they are difficult to study due to the low disease incidence and geographically dispersed patient populations, which has resulted in significant unmet clinical needs for patients with rare cancers. We assessed whether a patient-partnered research approach using online engagement can overcome these challenges, focusing on angiosarcoma, a sarcoma with an annual incidence of 300 cases in the United States. Here we describe the development of the Angiosarcoma Project (ASCproject), an initiative enabling US and Canadian patients to remotely share their clinical information and biospecimens for research. The project generates and publicly releases clinically annotated genomic data on tumor and germline specimens on an ongoing basis. Over 18 months, 338 patients registered for the ASCproject, which comprises a large proportion of all patients with angiosarcoma. Whole-exome sequencing (WES) of 47 tumors revealed recurrently mutated genes that included KDR, TP53, and PIK3CA. PIK3CA-activating mutations were observed predominantly in primary breast angiosarcoma, which suggested a therapeutic rationale. Angiosarcoma of the head, neck, face and scalp (HNFS) was associated with a high tumor mutation burden (TMB) and a dominant ultraviolet damage mutational signature, which suggested that for the subset of patients with angiosarcoma of HNFS, ultraviolet damage may be a causative factor and that immune checkpoint inhibition may be beneficial. Medical record review revealed that two patients with HNFS angiosarcoma had received off-label therapeutic use of antibody to the programmed death-1 protein (anti-PD-1) and had experienced exceptional responses, which highlights immune checkpoint inhibition as a therapeutic avenue for HNFS angiosarcoma. This patient-partnered approach has catalyzed an opportunity to discover the etiology and potential therapies for patients with angiosarcoma. Collectively, this proof-of-concept study demonstrates that empowering patients to directly participate in research can overcome barriers in rare diseases and can enable discoveries. A framework of patient-partnered research allows patients with angiosarcoma to share their samples and clinical records securely to accelerate molecular characterization of tumors and identification of therapeutic approaches.

Background: Patients with sarcoma often require individualized treatment strategies and are likely to receive aggressive immunosuppressive therapies, which may place them at higher risk for severe COVID-19. We aimed to describe demographics, risk factors, and outcomes for patients with sarcoma and COVID-19. Methods: We performed a retrospective cohort study of patients with sarcoma and COVID-19 reported to the COVID-19 and Cancer Consortium (CCC19) registry (NCT04354701) from 17 March 2020 to 30 September 2021. Demographics, sarcoma histologic type, treatments, and COVID-19 outcomes were analyzed. Results: of 281 patients, 49% (n = 139) were hospitalized, 33% (n = 93) received supplemental oxygen, 11% (n = 31) were admitted to the ICU, and 6% (n = 16) received mechanical ventilation. A total of 23 (8%) died within 30 days of COVID-19 diagnosis and 44 (16%) died overall at the time of analysis. When evaluated by sarcoma subtype, patients with bone sarcoma and COVID-19 had a higher mortality rate than patients from a matched SEER cohort (13.5% vs 4.4%). Older age, poor performance status, recent systemic anti-cancer therapy, and lung metastases all contributed to higher COVID-19 severity. Conclusions: Patients with sarcoma have high rates of severe COVID-19 and those with bone sarcoma may have the greatest risk of death.

Molecular profiling studies have enabled numerous discoveries for metastatic prostate cancer (MPC), but they have mostly occurred in academic medical institutions focused on select patient populations. We developed the Metastatic Prostate Cancer Project (MPCproject, mpcproject.org), a patient-partnered initiative to empower MPC patients living anywhere in the U.S. and Canada to participate in molecular research and contribute directly to translational discovery. Here we present clinicogenomic results from our partnership with the first 706 MPCproject participants. We found that a patient-centered and remote research strategy enhanced engagement with patients in rural and medically underserved areas. Furthermore, patient-reported data achieved 90% consistency with abstracted health records for therapies and provided a mechanism for patient-partners to share information about their cancer experience not documented in medical records. Among the molecular profiling data from 333 patient-partners (n = 573 samples), whole exome sequencing of 63 tumor samples obtained from hospitals across the U.S. and Canada and 19 plasma cell-free DNA (cfDNA) samples from blood donated remotely recapitulated known findings in MPC and enabled longitudinal study of prostate cancer evolution. Inexpensive ultra-low coverage whole genome sequencing of 318 cfDNA samples from donated blood revealed clinically relevant genomic changes like AR amplification, even in the context of low tumor burden. Collectively, this study illustrates the power of a longitudinal partnership with patients to generate a more representative clinical and molecular understanding of MPC.NoteTo assist our patient-partners and the wider MPC community interpret the results of this study, we have included a glossary of terms in the Supplementary Materials.

Background Hospitalized patients with COVID‐19 have increased risks of venous (VTE) and arterial thromboembolism (ATE). Active cancer diagnosis and treatment are well‐known risk factors; however, a risk assessment model (RAM) for VTE in patients with both cancer and COVID‐19 is lacking. Objectives To assess the incidence of and risk factors for thrombosis in hospitalized patients with cancer and COVID‐19. Methods Among patients with cancer in the COVID‐19 and Cancer Consortium registry (CCC19) cohort study, we assessed the incidence of VTE and ATE within 90 days of COVID‐19–associated hospitalization. A multivariable logistic regression model specifically for VTE was built using a priori determined clinical risk factors. A simplified RAM was derived and internally validated using bootstrap. Results From March 17, 2020 to November 30, 2020, 2804 hospitalized patients were analyzed. The incidence of VTE and ATE was 7.6% and 3.9%, respectively. The incidence of VTE, but not ATE, was higher in patients receiving recent anti‐cancer therapy. A simplified RAM for VTE was derived and named CoVID‐TE (Cancer subtype high to very‐high risk by original Khorana score +1, VTE history +2, ICU admission +2, D‐dimer elevation +1, recent systemic anti‐cancer Therapy +1, and non‐Hispanic Ethnicity +1). The RAM stratified patients into two cohorts (low‐risk, 0–2 points, n = 1423 vs. high‐risk, 3+ points, n = 1034) where VTE occurred in 4.1% low‐risk and 11.3% high‐risk patients (c statistic 0.67, 95% confidence interval 0.63–0.71). The RAM performed similarly well in subgroups of patients not on anticoagulant prior to admission and moderately ill patients not requiring direct ICU admission. Conclusions Hospitalized patients with cancer and COVID‐19 have elevated thrombotic risks. The CoVID‐TE RAM for VTE prediction may help real‐time data‐driven decisions in this vulnerable population.

Seventy percent of breast cancers express the estrogen receptor (ER), and agents that target the ER are the mainstay of treatment. However, virtually all people with ER+ breast cancer develop resistance to ER-directed agents in the metastatic setting. Beyond mutations in the ER itself, which occur in 25–30% of people treated with aromatase inhibitors1–4, knowledge about clinical resistance mechanisms remains incomplete. We identified activating HER2 mutations in metastatic biopsies from eight patients with ER+ metastatic breast cancer who had developed resistance to aromatase inhibitors, tamoxifen or fulvestrant. Examination of treatment-naive primary tumors in five patients showed no evidence of pre-existing mutations in four of five patients, suggesting that these mutations were acquired under the selective pressure of ER-directed therapy. The HER2 mutations and ER mutations were mutually exclusive, suggesting a distinct mechanism of acquired resistance to ER-directed therapies. In vitro analysis confirmed that the HER2 mutations conferred estrogen independence as well as—in contrast to ER mutations—resistance to tamoxifen, fulvestrant and the CDK4 and CDK6 inhibitor palbociclib. Resistance was overcome by combining ER-directed therapy with the irreversible HER2 kinase inhibitor neratinib. Activating HER2 mutations are shown to confer resistance to ER-directed therapies in patients with ER+ metastatic breast cancer. Drug resistance caused by HER2 mutations was overcome by combining ER-directed therapy with a HER2 kinase inhibitor.

BACKGROUND: Patients with cancer may be at high risk of adverse outcomes from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We analyzed a cohort of patients with cancer and coronavirus 2019 (COVID-19) reported to the COVID-19 and Cancer Consortium (CCC19) to identify prognostic clinical factors, including laboratory measurements and anticancer therapies. PATIENTS AND METHODS: Patients with active or historical cancer and a laboratory-confirmed SARS-CoV-2 diagnosis recorded between 17 March and 18 November 2020 were included. The primary outcome was COVID-19 severity measured on an ordinal scale (uncomplicated, hospitalized, admitted to intensive care unit, mechanically ventilated, died within 30 days). Multivariable regression models included demographics, cancer status, anticancer therapy and timing, COVID-19-directed therapies, and laboratory measurements (among hospitalized patients). RESULTS: A total of 4966 patients were included (median age 66 years, 51% female, 50% non-Hispanic white); 2872 (58%) were hospitalized and 695 (14%) died; 61% had cancer that was present, diagnosed, or treated within the year prior to COVID-19 diagnosis. Older age, male sex, obesity, cardiovascular and pulmonary comorbidities, renal disease, diabetes mellitus, non-Hispanic black race, Hispanic ethnicity, worse Eastern Cooperative Oncology Group performance status, recent cytotoxic chemotherapy, and hematologic malignancy were associated with higher COVID-19 severity. Among hospitalized patients, low or high absolute lymphocyte count; high absolute neutrophil count; low platelet count; abnormal creatinine; troponin; lactate dehydrogenase; and C-reactive protein were associated with higher COVID-19 severity. Patients diagnosed early in the COVID-19 pandemic (January-April 2020) had worse outcomes than those diagnosed later. Specific anticancer therapies (e.g. R-CHOP, platinum combined with etoposide, and DNA methyltransferase inhibitors) were associated with high 30-day all-cause mortality. CONCLUSIONS: Clinical factors (e.g. older age, hematological malignancy, recent chemotherapy) and laboratory measurements were associated with poor outcomes among patients with cancer and COVID-19. Although further studies are needed, caution may be required in utilizing particular anticancer therapies. CLINICAL TRIAL IDENTIFIER: NCT04354701.

When the COVID-19 pandemic began, formal frameworks to collect data about affected patients were lacking. The COVID-19 and Cancer Consortium (CCC19) was formed to collect granular data on patients with cancer and COVID-19 at scale and as rapidly as possible. CCC19 has grown from five initial institutions to 125 institutions with >400 collaborators. More than 5,000 cases with complete baseline data have been accrued. Future directions include increased electronic health record integration for direct data ingestion, expansion to additional domestic and international sites, more intentional patient involvement, and granular analyses of still-unanswered questions related to cancer subtypes and treatments.

IMPORTANCE: Research into the genetic and genomic (“genomics”) foundations of disease is central to our understanding of disease prevention, early detection, diagnostic accuracy, and therapeutic intervention. Inequitable participation in genomics research by historically excluded populations limits the ability to translate genomic knowledge to achieve health equity and ensure that findings are generalizable to diverse populations. OBSERVATIONS: We propose a novel framework for promoting diversity, equity, and inclusion in genomics research. Building on principles of community-based participatory research and collective impact frameworks, the framework can guide our understanding of the social, cultural, health system, policy, community, and individual contexts in which engagement and genomics research are being done. Our framework highlights the involvement of a multistakeholder team, including the participants and communities to be engaged, to ensure robust methods for recruitment, retention, return of genomic results, quality of engagement, follow-up, and monitoring of participants. CONCLUSIONS AND RELEVANCE: The proposed engagement framework will guide investigators in optimizing equitable representation in research and enhancing the rigor of genomics investigation.

Non-Hispanic Black individuals experience a higher burden of COVID-19 than the general population; hence, there is an urgent need to characterize the unique clinical course and outcomes of COVID-19 in Black patients with cancer.To investigate racial disparities in severity of COVID-19 presentation, clinical complications, and outcomes between Black patients and non-Hispanic White patients with cancer and COVID-19.This retrospective cohort study used data from the COVID-19 and Cancer Consortium registry from March 17, 2020, to November 18, 2020, to examine the clinical characteristics and outcomes of COVID-19 in Black patients with cancer. Data analysis was performed from December 2020 to February 2021.Black and White race recorded in patient's electronic health record.An a priori 5-level ordinal scale including hospitalization intensive care unit admission, mechanical ventilation, and all-cause death.Among 3506 included patients (1768 women [50%]; median [IQR] age, 67 [58-77] years), 1068 (30%) were Black and 2438 (70%) were White. Black patients had higher rates of preexisting comorbidities compared with White patients, including obesity (480 Black patients [45%] vs 925 White patients [38%]), diabetes (411 Black patients [38%] vs 574 White patients [24%]), and kidney disease (248 Black patients [23%] vs 392 White patients [16%]). Despite the similar distribution of cancer type, cancer status, and anticancer therapy at the time of COVID-19 diagnosis, Black patients presented with worse illness and had significantly worse COVID-19 severity (unweighted odds ratio, 1.34 [95% CI, 1.15-1.58]; weighted odds ratio, 1.21 [95% CI, 1.11-1.33]).These findings suggest that Black patients with cancer experience worse COVID-19 outcomes compared with White patients. Understanding and addressing racial inequities within the causal framework of structural racism is essential to reduce the disproportionate burden of diseases, such as COVID-19 and cancer, in Black patients.

Patients with cancer have been disproportionately affected by the COVID-19 pandemic. This effect has included the adverse outcomes in patients with cancer who develop COVID-19, the impact of the COVID-19 pandemic on the delivery of cancer care, and the severe disruption to cancer research. However, patients with cancer are a heterogeneous population, and recent studies have now documented factors that allow risk stratification of patients with cancer in order to optimize care. In this review, we highlight data at the intersection of COVID-19 and cancer, including the biological interplay between the two diseases and practical recommendations for the treatment of patients with cancer during the pandemic. We additionally discuss the potential long-lasting impact of the pandemic on cancer care due to its deleterious effect on cancer research, as well as biological insights from the cancer research community that could help develop novel therapies for all patients with COVID-19.

Significance The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of COVID-19, a major pandemic that threatens millions of human lives and the global economy. We identified a large number of mammals that can potentially be infected by SARS-CoV-2 via their ACE2 proteins. This can assist the identification of intermediate hosts for SARS-CoV-2 and hence reduce the opportunity for a future outbreak of COVID-19. Among the species we found with the highest risk for SARS-CoV-2 infection are wildlife and endangered species. These species represent an opportunity for spillover of SARS-CoV-2 from humans to other susceptible animals. Given the limited infectivity data for the species studied, we urge caution not to overinterpret the predictions of the present study., The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of COVID-19. The main receptor of SARS-CoV-2, angiotensin I converting enzyme 2 (ACE2), is now undergoing extensive scrutiny to understand the routes of transmission and sensitivity in different species. Here, we utilized a unique dataset of ACE2 sequences from 410 vertebrate species, including 252 mammals, to study the conservation of ACE2 and its potential to be used as a receptor by SARS-CoV-2. We designed a five-category binding score based on the conservation properties of 25 amino acids important for the binding between ACE2 and the SARS-CoV-2 spike protein. Only mammals fell into the medium to very high categories and only catarrhine primates into the very high category, suggesting that they are at high risk for SARS-CoV-2 infection. We employed a protein structural analysis to qualitatively assess whether amino acid changes at variable residues would be likely to disrupt ACE2/SARS-CoV-2 spike protein binding and found the number of predicted unfavorable changes significantly correlated with the binding score. Extending this analysis to human population data, we found only rare (frequency

Background: The Metastatic Breast Cancer Project (MBCproject) is an ongoing research study that directly engages patients (pts) through social media and advocacy groups, and empowers them to share their biospecimens, clinical history, and experiences. The goal is to create a publicly available dataset of linked clinicogenomic and pt-reported data to enable research. From 2015-10-20 to 2020-3-31, 3,245 MBC pts who received treatment at >1,700 institutions, consented to share medical records, pt-reported data, and tumor/saliva/blood samples and to have genomic analysis performed. Here, we describe an analysis of the clinical and genomic features in this initial MBCproject cohort. Methods: We performed whole exome sequencing (WES) on 379 tumors (with matched germline) from 301 pts, 377 germline samples and RNA sequencing (RNA-seq) from 200 tumors from 141 pts. In 14 pts, we characterized 2 or more serial tumor biopsies. WES data was analyzed for mutations and copy number variants. RNA-seq data was used to call fusions, research-grade PAM50, and gene set enrichment scores. Medical records and pt-reported data were abstracted to create detailed clinical record for each pt. Results: WES of 249 metastatic tumors identified 34 cancer genes (e.g., TP53, PIK3CA, CDH1, PTEN, AKT1, NF1, ESR1) that were significantly recurrently altered. Potential clinically actionable alterations were identified in 39% of metastatic tumors. 45 tumors (22.5%) had fusions with known functional effects and 24 (12%) had in-frame fusions in key cancer genes like FANCD2 (3), FGFR3 (2), ESR1 (1), BRAF (1), and NCOR1 (1). PAM50 classification suggested depletion of Luminal A subtype in this cohort compared to TCGA breast cancer cohort (p-value Citation Format: Esha Jain, Dewey Kim, Jorge Gomez Tejeda Zanudo, Sara Balch, Mary McGillicuddy, Brett N. Tomson, Tania G. Hernandez, Beena S. Thomas, Daniel L. Abravanel, Shahrayz Shah, Rafael Ramos, Delia Sosa, Ilan Small, Lauren Sterlin, Sarah Winnicki, Colleen Nguyen, Micheal Dunphy, Elana Anastasio, Todd R. Golub, Corrie A. Painter, Nikhil Wagle. The metastatic breast cancer project - Expanding the clinical, genomic, and transcriptomic landscape of metastatic breast cancer through patient-partnered research [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr PD6-02.

Background: The Metastatic Breast Cancer Project is a nationwide research initiative that directly engages patients through social media and advocacy groups and seeks to empower them to share their samples and clinical information to accelerate research. Because the vast majority of patients are treated in the community setting, we sought to determine the feasibility of remotely obtaining tumor and saliva samples as well as medical records from a large cohort of metastatic breast cancer (MBC) patients who receive their care in diverse settings around the country. Methods: In collaboration with patients and advocacy groups, we developed a website to allow MBC patients across the U.S. to participate. Enrolled patients are sent a saliva kit and asked to mail back a saliva sample, which is used to extract germline DNA. We contact participants' medical providers and obtain medical records and part of their tumor biopsy. Whole exome and transcriptome sequencing is performed on tumor and germline samples. Clinically annotated genomic data are used to identify mechanisms of response and resistance to therapies. The database will be shared widely with researchers. Study updates and discoveries are shared with participants regularly. Results: In the first 8 months, 2285 MBC patients from all 50 states enrolled. 2163 (95%) completed the 16-question survey about their cancer, treatments, and demographic information. 1232 completed the online consent form permitting acquisition and analysis of medical records, tumor tissue, and saliva samples. 556 saliva samples have been received. Initial medical record and tumor sample requests have been made for patients who have provided saliva samples. To date, we have obtained medical records from 102 patients (93% success rate) and tumor samples from 32 patients (77% success rate). Whole exome and transcriptome sequencing has been successfully completed on initial samples received and is ongoing for additional samples. Conclusions: Partnering directly with patients through social media and advocacy groups enables rapid identification of thousands of patients willing to share tumors, saliva, and medical records to accelerate research. This approach allows for rapid identification of patients with rare phenotypes such as extraordinary responders, who have been challenging to identify with traditional approaches. Remote acquisition of medical records, saliva samples, and tumor tissue for patients located throughout the U.S. is feasible. Genomic analysis and medical record abstraction for these patients is underway. As data is generated, a clinically annotated database will be shared widely with the research community. Citation Format: Painter CA, Anastasio E, Krevalin M, Kim D, Larken K, Lennon N, Frank E, Winer EP, Lander ES, Golub T. The metastatic breast cancer project: Translational genomics through direct patient engagement [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-05-13.

Kasheta et al. report the identification of T reg–like cells in zebrafish, a means to track and live-image these cells, and foxp3a-deficient mutants that display lymphoproliferation, severe inflammation, and other hallmarks of T reg deficiency syndromes., Regulatory T (T reg) cells are a specialized sublineage of T lymphocytes that suppress autoreactive T cells. Functional studies of T reg cells in vitro have defined multiple suppression mechanisms, and studies of T reg–deficient humans and mice have made clear the important role that these cells play in preventing autoimmunity. However, many questions remain about how T reg cells act in vivo. Specifically, it is not clear which suppression mechanisms are most important, where T reg cells act, and how they get there. To begin to address these issues, we sought to identify T reg cells in zebrafish, a model system that provides unparalleled advantages in live-cell imaging and high-throughput genetic analyses. Using a FOXP3 orthologue as a marker, we identified CD4-enriched, mature T lymphocytes with properties of T reg cells. Zebrafish mutant for foxp3a displayed excess T lymphocytes, splenomegaly, and a profound inflammatory phenotype that was suppressed by genetic ablation of lymphocytes. This study identifies T reg–like cells in zebrafish, providing both a model to study the normal functions of these cells in vivo and mutants to explore the consequences of their loss.

Despite rare cancers accounting for 25% of adult tumors

Angiosarcoma is a highly aggressive cancer of blood vessel-forming cells with high fatality and few effective treatment options. It is both rare and heterogenous, making large, well powered genomic studies nearly impossible. In dogs, angiosarcoma is common, with breeds like the golden retriever carrying heritable genetic factors that put them at very high risk. If the clinical similarity of canine and human angiosarcoma reflects shared genomic etiology, dogs could be a critically needed model for advancing angiosarcoma research. We assessed the genomic landscape of canine angiosarcoma via whole exome sequencing (47 golden retriever angiosarcomas) and RNA sequencing (74 angiosarcomas from multiple breeds). The predominant mutational signature was the age-associated deamination of cytosine to thymine, and somatic coding mutations occurred most frequently in the tumor suppressorTP53(59.6% of cases) as well as two genes in the PI3K pathway: the oncogenePIK3CA(29.8%) and its regulatory subunitPIK3R1(8.5%). We compared the canine data to human data recently released by The Angiosarcoma Project, and found the same genes and many of the same pathways significantly enriched for somatic mutations, most notably protein kinases, glycoproteins, fibronectin Type III domains, EGF-like domains, and cell adhesion proteins such as cadherins. As in human angiosarcoma,CDKN2A/Bwas recurrently deleted andVEGFA, KDR, and KITrecurrently gained. Canine angiosarcoma closely models human angiosarcoma on a genomic level, and is a powerful tool for investigating the pathogenesis of this devastating disease.

Background: Overall, patients with cancer experience a greater risk of adverse outcomes following SARS-CoV-2 infection; however, little is known for those with BC. Methods: CCC19 (NCT04354701) is an international cohort study aimed at investigating the impact of COVID-19 in patients with a history of or active cancer using de-identified data on patient demographics, cancer history, clinical course and outcomes of COVID-19. The current analysis includes patients from U.S. and Canada with invasive BC and laboratory-confirmed SARS-CoV-2 entered between March 17, 2020 and July 2, 2020. Co-primary outcomes were hospitalization during COVID-19 illness and 30-day all-cause mortality. Frequencies for categorical variables and medians (range) for continuous variables were estimated. Final presentation will include bivariable and multivariable Cox proportional hazards regression analysis to identify risk factors (including BC subtypes and therapies, for which data collection is ongoing) associated with 30-day all-cause mortality and severe COVID-19 illness (composite of any hospitalization requiring supplemental oxygen, admission to an intensive care unit [ICU], use of mechanical ventilation, or death). Results: During the study period, a total of 2683 patients with cancer and COVID-19 were accrued in the CCC19 registry including 529 (20%) with invasive BC. Among patients with BC, 352 (67%) were 60 years or older; 518 (98%) were women; 275 (52%) non-Hispanic White, 116 (22%) non-Hispanic Black, 70 (13%) Hispanic, 56 (11%) in other categorizations; 178 (34%) had a smoking history; 75 (14%) ECOG performance status ≥2; 191 (36%) with >2 active comorbidities; 64 (12%) with AJCC stage IV disease at BC diagnosis; and 267 (50%) were on anti-cancer treatment including systemic therapy, radiation, or surgery within 3 months of COVID-19 diagnosis. At least 323 (61%) patients with BC had 30-day follow-up after COVID-19 diagnosis, and 35 (7%) had 90-day follow-up. COVID-19 illness at initial diagnosis required outpatient care in 288 (54%), inpatient care in 193 (36%), and ICU care in 40 (8%). Overall, 247 (47%) were hospitalized and 30-day all-cause mortality was 9%. 30-day all-cause mortality rates by receipt of major BC treatment modalities (within past 3 months) were: 10% for those on cytotoxic systemic therapy vs 5% and 12% for noncytotoxic systemic therapy and local therapy, respectively. The table shows hospitalization and mortality outcomes by major demographic and BC treatment strata. The final presentation will incorporate the latest patient accrual and evaluate independent clinical risk factors associated with serious COVID-19 outcomes in patients with BC. Conclusions: This represents the largest study to date of COVID-19 outcomes in patients with invasive BC. Nearly half of the patients with BC required hospitalization during their COVID-19 disease course and we observed a 9% 30-day all-cause mortality. Submitted on behalf of the COVID-19 and Cancer Consortium (ccc19us.org) Table 1. COVID-19 related hospitalization and 30-day all-cause mortality for all patients with invasive BCNAny Hospitalization30-day all-cause MortalityN% [95% CI]N% [95% CI]Total population52924747 [42-51]499 [7-12]Age219112968 [60-74]2915 [10-21]Treatment IntentCurative1866434 [28-42]95 [2-9]Palliative743953 [41-64]1216 [9-27]Cancer StatusRemission/NED33115447 [41-52]247 [5-11]Active disease, stable or responding to treatment1194840 [31-50]76 [2-12]Active disease, progressing372773 [56-86]1130 [16-47]Treatment Modality (within 3 months)Cytotoxic chemotherapy833542 [31-54]810 [4-18]Noncytotoxic therapy1856435 [28-42]105 [3-10]Local therapy (surgery or radiation)341750 [32-68]412 [3-27] Citation Format: Ali Raza Khaki, Dimpy P Shah, Maryam B Lustberg, Melissa K Accordino, Daniel G Stover, Gayathri Nagaraj, Donna R Rivera, Edith A Perez, Sara M Tolaney, Jeffrey Peppercorn, Petros Grivas, Jeremy L Warner, Corrie A Painter, Gilberto de Lima Lopes, Jr, Solange Peters, Michael A Thompson, Toni K Choueiri, Brian I Rini, Gary H Lyman, Nicole M Kuderer, Shaveta Vinayak. Characteristics and outcomes of SARS-CoV-2 infection in patients with invasive breast cancer (BC) from the COVID-19 and cancer consortium (CCC19) cohort study [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS7-01.

Over the past decade, genomic characterization of tumors has shed enormous light on the molecular underpinnings of cancer. These discoveries have led to the development of novel therapies and preventive measures that have already revolutionized cancer care. Despite this progress, the genomics of metastatic breast cancer (MBC), one of the leading causes of cancer death in the U.S., remains poorly understood. The challenge in studying tumor samples from patients with MBC has been that the tumors from most patients are not available for research, largely because the vast majority of patients are cared for in community settings where genomics studies are not typically conducted. To address this, we have launched a nationwide study, The Metastatic Breast Cancer Project, which seeks to empower patients to accelerate cancer research through sharing their samples and clinical information. We have developed an outreach program in collaboration with MBC advocacy organizations to connect MBC patients around the country with genomics research performed at the Broad Institute, allowing them to participate regardless of where they live. Working with MBC patients and advocates, we designed a website (www.mbcproject.org) with an online questionnaire that allows patients with MBC to provide information about themselves and their cancer. Based on their answers, patients are offered an electronic consent form that explains the risks and benefits of the study and asks for permission to obtain a portion of their stored tumor tissue, a saliva sample, and copies of their medical records. For patients who consent, our clinical research team contacts their physicians and obtains copies of their medical records, which are reviewed to confirm eligibility. Enrolled patients are sent a saliva kit and asked to mail back a saliva sample, which is used to extract germline DNA. The clinical research team also contacts the patient's pathology department and requests a portion of the tumor to be sent to the Broad Institute for genomic analysis. Whole exome and transcriptome sequencing is performed on tumor and germline DNA. Sequencing data are linked to de-identified clinical information, and the resulting data are used to identify drivers of tumorigenesis, mechanisms of response and resistance to therapies, and diagnostic, prognostic, and therapeutic biomarkers. The database of clinically annotated genomic information will be shared with the NIH and the cancer research community. Study updates and discoveries are shared at regular intervals with all patients who complete the initial questionnaire. This direct-to-patient approach should be particularly enabling for the identification of patients with rare phenotypes or clinical behavior. For this reason, the first cohorts being studied are patients with extraordinary responses to therapies and patients who present with de novo MBC. Additional cohorts will be added in the future, including young women with MBC and patients with drug-resistant MBC. This project seeks to establish a patient-researcher partnership to accelerate genomic discoveries and improve outcomes in MBC, and may ultimately serve as a means to build a new clinical and translational research model for all patients with cancer. Citation Format: Wagle N, Painter CA, Ilzarbe M, Van Allen EM, Frank E, Oh C, Krevalin M, Lloyd M, Anderka K, Kryukov G, Boehm JS, Winer E, Lander ES, Golub TR. The metastatic breast cancer project: A national direct-to-patient research initiative to accelerate genomics research. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr OT2-05-03.

Breast cancer is the leading cause of cancer-related mortality for Latinx women in the US. Compounding this challenge is low representation of Latinx patients (pts) in cancer research studies. Neglecting Latinx participation limits scientific understanding and the development of effective therapies for all pts. To address this disparity and increase research accessibility, we collaborated with Latinx community (comm) members and translated all aspects of an existing patient-partnered research project, The Metastatic Breast Cancer Project (MBCproject), into Spanish. The MBCproject (MBCproject.org) is a research study that directly engages pts through social media and advocacy groups, empowering pts to share their samples, clinical information, and experiences. Despite having 3,300 consented participants, only 3.7% (123) identify as Hispanic, Latinx, or Spanish. With the Latinx population increasing in the US and cancer’s impact on the comm, it is imperative that Latinx individuals participate in cancer research. Native Spanish speaking members on the MBCproject team leveraged the existing MBCproject model of direct collaboration with pt communities to translate pt-facing materials. Pts and pt advocates provided feedback on site content, project name, surveys, and biospecimen kit instructions through video calls with team staff. Over 17 months, 6 focus groups were held with 9 members of the comm, assessing 6 different material items. Iterations of the materials discussed were shared via email to complete the process. Proposed Spanish language dialect, pronoun formality, and transparency in project content were also reviewed to ensure messaging resonated with the broader Latinx comm. Following comm review, modifications were integrated into materials. A Mexican- Spanish dialect and formal pronouns were chosen to be used across all materials. The project name remained to maintain continuity across languages. Distinct feedback included simplified terminology and materials that could be shared with their health care provider. Clarity in tissue acquisition, privacy of data collected, and participation requirements was also requested. Attendance of study staff at Latinx cancer disparities research conferences revealed interest amongst investigators for more comprehensive demographic data collection of Latinx pts in studies, leading to the development of more detailed race and ethnicity questions in our intake survey. Finalized project materials have been submitted for IRB approval and expected to be launched at mbcprojectenespanol.org in Fall 2020. This partnered approach has led to an inclusive set of materials embraced by the Latinx pts and pt advocates who have helped us develop the MBCproject in Spanish. This is a foundational pilot that will allow Spanish speaking participants to engage in cancer research without a language barrier and contribute to the acceleration of scientific discoveries that impacts their community. Citation Format: Tania G. Hernandez, Sara Balch, Jorge Buendia- Buendia, Jorge Gomez Tejeda Zanudo, Mary McGillicuddy, Colleen M. Nguyen, Foxy Robinson, Corrie Painter, Elana Anastasio, Michael Dunphy, Nikhil Wagle. The Metastatic Breast Cancer Project in Spanish: Developing a Spanish language patient-partnered research project with the Latinx community through culturally appropriate materials [abstract]. In: Proceedings of the AACR Virtual Conference: Thirteenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2020 Oct 2-4. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(12 Suppl):Abstract nr PO-015.

Background: The Metastatic Breast Cancer Project (MBCproject) is a research study that directly engages patients (pts) through social media and advocacy groups, and empowers them to share their samples, clinical information, and experiences. The goal is to create a publicly available dataset of linked genomic, clinical, and pt-reported data to enable research. Methods: In collaboration with pts, advocates, and advocacy groups, a website (MBCproject.org) was developed that allows pts with metastatic breast cancer (MBC) anywhere in the U.S. or Canada to register. Registered pts are sent an online consent form that asks for permission to obtain and analyze their medical records and samples. Once enrolled, pts are sent a saliva kit and a blood kit and asked to mail back a saliva sample, which is used to extract germline DNA, and/or a blood sample, which is used to extract germline DNA and cell free DNA (cfDNA). We contact participants’ medical providers and obtain medical records and a portion of their stored tumor biopsies. Whole exome sequencing (WES) is performed on tumor DNA, germline DNA, and cfDNA; transcriptome sequencing (RNA-seq) is performed on tumor RNA. Medical records and pt-reported data are abstracted to create a detailed clinical record for each pt. All de-identified data are shared regularly via public databases (cbioportal.org, mbcproject.org, dbGaP, NCI Genomic Data Commons) without restrictions. Study updates are shared with participants regularly. Results: From 10/20/15-7/8/19, 5357 women and men with MBC registered. 3290 pts receiving care at over 1700 different institutions consented to share medical records and tumor/saliva/blood samples, and to have genomic analysis performed. Details of clinical data collection, biospecimen acquisition, and genomic data generation to date are outlined in the Table. WES from 463 tumors obtained from 326 pts have been generated (with matched germline WES), including 61 pts with 2 timepoints, 19 pts w 3 timepoints, and 11 pts w 4+ timepoints. 278 tumor exomes were from the breast/regional lymph nodes, 63 from distant metastatic sites and 122 from cfDNA. 110 tumor exomes were from samples obtained before the diagnosis of MBC, 258 from after the diagnosis of MBC, and 95 to be determined (TBD). 161 tumor exomes were obtained prior to any therapy, 204 following some therapy, and 98 TBD. Clinically annotated genomic data are used to study specific pt cohorts (including rare subsets and outliers) and to identify mechanisms of response and resistance to therapies. Examples of the clinical and genomic analyses that will be presented include: - Pts diagnosed 5 yrs after diagnosis (830 pts enrolled; 77 with tumor WES) - Long-term survivors, >10 yrs with MBC (159 pts enrolled; 11 with tumor WES) - Resistance to CDK4/6 inhibitors (709 pts enrolled; 148 with tumor WES) Conclusions: Partnering directly with pts enables rapid identification of thousands of pts willing to share tumors, blood, saliva, and medical records to accelerate research. This approach allows for identification of patients with specific phenotypes, who have been challenging to identify with traditional approaches. Remote acquisition of medical records and saliva/blood/tumor samples is feasible. This clinically annotated dataset is a shared resource for the research community. Table 1Clinical data collection, biospecimen acquisition, and genomic data generation:NumberConsent signed3290 ptsSurvey #1 submitted3290 pts(demographics, diagnosis details, receptor status, clinical experiences)Survey #2 submitted1435 pts(pathology details, sites of metastasis, treatments with start and stop dates)Medical record received1307 ptsSaliva sample received1976 ptsBlood sample received1121 ptsTumor samples received482 tumor samples from 346 ptsDigital image of tumor slide H&E generated482 tumor samplesWES from germline complete310 germline samplesWES from tumor sample complete341 tumor samplesRNA-seq from tumor sample complete229 tumor samplesULP-WGS from cfDNA complete947 blood samplesWES from circulating tumor DNA complete122 blood samples Citation Format: Nikhil Wagle, Corrie Painter, Elana Anastasio, Michael Dunphy, Mary McGillicuddy, Esha Jain, Tania G Hernandez, Sara Balch, Beena Thomas, Dewey Kim, Alyssa L. Damon, Shahrayz Shah, Brett N. Tomson, Rachel Stoddard, Colleen Nguyen, Jorge Buendia-Buendia, Ofir Cohen, Jorge Gomez Tejeda Zanudo, Netsanet Tsegai, Lauren Sterlin, Ulcha Fergie Ulysse, Kathryn Sine, Oyin Alao, Jacqueline Lucia, Eric S. Lander, Todd R. Golub. The metastatic breast cancer project: Generating the clinical and genomic landscape of metastatic breast cancer through patient-partnered research [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr PD8-01.

Rare cancers pose unique challenges to research due to their low incidence. Barriers include a scarcity of tissue and experimental models to enable basic research and insufficient patient accrual for clinical studies. Consequently, an understanding of the genetic and cellular features of many rare cancer types and their associated vulnerabilities has been lacking. However, new opportunities are emerging to facilitate discovery of therapeutic targets in rare cancers. Online platforms are allowing patients with rare cancers to organize on an unprecedented scale, tumor genome sequencing is now routinely performed in research and clinical settings, and the efficiency of patient-derived model generation has improved. New CRISPR/Cas9 and small-molecule libraries permit cancer dependency discovery in a rapid and systematic fashion. In parallel, large-scale studies of common cancers now provide reference datasets to help interpret rare cancer profiling data. Together, these advances motivate consideration of new research frameworks to accelerate rare cancer target discovery.

Background: Approximately 5-10% of newly diagnosed breast cancers (BC) are de novo MBC, which means that metastatic disease was identified at the time of initial diagnosis. Patients with de novo MBC are underrepresented in currently available genomic studies. In The Cancer Genome Atlas (TCGA) dataset, only 15 out of ˜980 BC patients can be classified as having de novo MBC. The objective of this study is to analyze the genomic landscape of de novo MBC and to study the genomic differences of this cohort with early stage BC. To enhance our ability to study de novo MBC, we utilized data from the Metastatic Breast Cancer Project (MBCproject), a patient-partnered research project that aims to generate a large public database of clinical, genomic, and patient reported data (PRD) from patients with MBC. Methods: We defined de novo MBC as patients diagnosed with metastatic disease less than 4 months after their initial diagnosis with BC.Out of 127 patients in the MBCproject with publicly released whole exome sequencing (WES) data, we identified 33 patients with de novo MBC. We combined this data with 15 de novo MBC patients in TCGA. For patients with de novo MBC with multiple tumor biopsies available, we used WES from breast biopsies to enable appropriate comparison to the early stage biopsies. Somatic mutations were evaluated and significantly recurring genes were identified using MutSig2CV. We compared the mutations found in the de novo cohort with early stage tumors. 10 patients in the de novo MBC cohort had paired simultaneous primary and metastatic biopsies; genomic alterations in these samples were compared. Finally, we used RNA sequencing data to compare cytolytic signatures among the de novo and early stage biopsies. Results: Among the 48 patients analyzed the receptor subtype distribution was: HR+/HER2-(23), HR+/HER2+(13), HR-/HER2+(2), HR-/HER2-(3), HR+/HER2 unknown(5), and HR-/HER2 unknown(2). Histology subtype distribution was as follows: IDC(39), MDLC(6), ILC(2) and Other (1). Significantly recurrent genes in the de novo MBC cohort (q Gene% Mutation Rate in De Novo MBC (N=48)% Mutation rate in Early Stage BC (N= 997)p-valuePTEN10.403.510.0324EGFR6.250.500.00435MDM44.170.300.0189 Conclusions: Our initial results highlight genomic differences between de novo MBC and early stage BC, including increased frequency of PTEN, EGFR, and MDM4 mutations. Enrichment of PTEN mutations (implicated in tumor immune surveillance), and downregulation of cytolytic signature potentially suggests that de novo MBC may have immunosuppressive tumor microenvironment. To date, ˜1200 patients with self-reported de novo MBC have registered for the MBCproject. We anticipate that additional study of genomic and clinical data from these patients will greatly improve our understanding of de novo MBC. Citation Format: Jain E, Kim D, Buendia JB, Cohen O, Sousa RB, Anastasio E, Dunphy M, McGillicuddy M, Stoddard R, Balch S, Thomas B, Di Lascio S, Tomson BN, Nguyen C, Painter C, Wagle N. The genomic landscape of de novo metastatic breast cancer (MBC) [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr PD9-03.

Mammalian class II major histocompatibility (MHCII) proteins bind peptide antigens in endosomal compartments of antigen-presenting cells. The nonclassical MHCII protein HLA-DM chaperones peptide-free MHCII, protecting it against inactivation, and catalyzes peptide exchange on loaded MHCII. Another nonclassical MHCII protein, HLA-DO, binds HLA-DM and influences the repertoire of peptides presented by MHCII proteins. However, the mechanism by which HLA-DO functions is unclear. Here we have used X-ray crystallography, enzyme kinetics and mutagenesis approaches to investigate human HLA-DO structure and function. In complex with HLA-DM, HLA-DO adopts a classical MHCII structure, with alterations near the α subunit's 3₁₀ helix. HLA-DO binds to HLA-DM at the same sites implicated in MHCII interaction, and kinetic analysis showed that HLA-DO acts as a competitive inhibitor. These results show that HLA-DO inhibits HLA-DM function by acting as a substrate mimic, and the findings also limit the possible functional roles for HLA-DO in antigen presentation.

Recent structural characterizations of classical and non-classical major histocompatibility complex class II (MHCII) proteins have provided a view into the dynamic nature of the MHCII-peptide binding groove and the role that structural changes play in peptide loading processes. Although there have been numerous reports of crystal structures for MHCII-peptide complexes, a detailed analysis comparing all the structures has not been reported, and subtle conformational variations present in these structures may not have been fully appreciated. We compared the 91 MHCII crystal structures reported in the PDB to date, including an HLA-DR mutant particularly susceptible to DM-mediated peptide exchange, and reviewed experimental and computational studies of the effect of peptide binding on MHCII structure. These studies provide evidence for conformational lability in and around the α-subunit 3-10 helix at residues α48-51, a region known to be critical for HLA-DM-mediated peptide exchange. A biophysical study of MHC-peptide hydrogen bond strengths and a recent structure of the non-classical MHCII protein HLA-DO reveal changes in the same region. Conformational variability was observed also in the vicinity of a kink in the β-subunit helical region near residue β66 and in the orientation and loop conformation in the β2 Ig domain. Here, we provide an overview of the regions within classical and non-classical MHCII proteins that display conformational changes and the potential role that these changes may have in the peptide loading/exchange process.

Despite the reduction in cancer recurrence and mortality provided by therapies that target the estrogen receptor (ER), resistant ER+ breast cancer remains the most common cause of breast cancer death. Beyond mutations in ER in 25-30% of patients treated with aromatase inhibitors, which deplete circulating estrogen, our understanding of clinical mechanisms of resistance to agents that target the ER remains incomplete. We used whole exome sequencing (WES) of metastatic biopsies to identify mechanisms of resistance in patients with ER+ metastatic breast cancer (MBC) who had developed resistance to ER-directed agents, including aromatase inhibitors, tamoxifen, and fulvestrant. We noted mutations in human epidermal growth factor receptor 2 (HER2) in metastatic biopsies from 12 patients out of 168. Of these, eight mutations had previously been described as activating. Examination of the treatment-naïve primary tumors in the five patients with activating mutants where WES from the matched treatment-naïve primary tumor was available revealed no evidence of pre-existing mutations in four of the five patients, suggesting that these four mutations were acquired under the selective pressure of ER-directed therapy. These acquired HER2 mutations were mutually exclusive with ER mutations, suggesting a distinct mechanism of resistance to ER-directed therapies. In vitro analysis through expression in ER+/HER2- cell lines confirmed that these mutations conferred estrogen independence. In addition, and in contrast to ER mutations, these HER2 mutations resulted in resistance to tamoxifen, fulvestrant, and the CDK4/6 inhibitor palbociclib. The mutants result in increased AKT and ERK phosphorylation in ER+ cell lines, while simultaneously repressing ER levels and ER-dependent transcriptional targets. One mutation observed in two patients, S653C, occurring in the transmembrane domain and not previously observed in breast cancer, was shown to likely function through constitutive dimerization, a mechanism of activation not previously described for this mutation. Resistance caused by all four mutations was overcome by combining ER-directed therapy with the irreversible HER2 kinase inhibitor neratinib, suggesting a novel effective treatment strategy in these patients. Thus, we have shown that acquired activating HER2 mutations can confer endocrine resistance in ER+/HER2- breast cancer, and that such resistance can be effectively reversed by combination therapies that include an anti-HER2 inhibitor. Citation Format: Utthara Nayar, Ofir Cohen, Christian Kapstad, Adrienne Waks, Seth A. Wander, Corrie Painter, Samuel Freeman, Priyanka Ram, Nicole Persky, Lori Marini, Karla Helvie, Nelly Oliver, Cynthia X. Ma, Eric P. Winer, Nancy U. Lin, Nikhil Wagle. Acquired HER2 mutations in ER+ metastatic breast cancer confer resistance to ER-directed therapies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4952.

Angiosarcoma (AS) is an exceedingly rare soft tissue sarcoma, with an incidence of 300 cases/yr and a 5-year disease-specific survival of 30%. The low incidence has impeded large-scale research efforts that may lead to improved clinical outcomes. To address this, we launched a nationwide clinical-genomics study in order to empower patients to accelerate research by sharing their normal and tumor samples and clinical information remotely. Patients can access the study through an online portal (ASCproject.org). Enrolled patients are mailed saliva and blood draw kits. The study team obtains medical records and stored FFPE tumor samples. All received FFPE samples are examined by an expert pathologist to confirm a diagnosis of angiosarcoma. In order to validate that our processes would enable the generation of a robust dataset from tissues acquired from multiple institutions, we sought to characterize previously described genes known to be altered in angiosarcoma (e.g., TP53, NF1, KDR, BRCA2, MET, ARID1A, POT1, BRCA1, ASXL1, KDM6A, BRAF, SETD2, PTPRB, NRAS). A total of 251 patients have enrolled since the project launched in March of 2017. Primary locations of AS are primary breast 59 (25%), breast with prior radiation 45 (19%), head/face/neck/scalp 52 (22%), bone/limb 26 (11%), abdomen 5 (2%), heart 5 (2%), lung 2 (1%), liver 1 (1%), lymph 1 (0.4%), multiple locations 25 (11%), and other locations 12 (5%); 107 (52%) reported being disease free at the time of enrollment. To date, we have received 129 saliva kits, 106 medical records, 19 blood samples, and 36 tissue samples. Whole-exome sequencing (WES) was performed on 21 FFPE/saliva matched pairs with a goal mean target coverage of 150x for tumors. Ultra-low pass whole-genome sequencing (0.1x) was performed on cell free DNA (cfDNA) from plasma in order to determine tumor fraction. Of 10 cfDNA samples sequenced, 4 samples met criteria to perform WES. Additionally, transcriptome sequencing was performed on 9 FFPE samples. Sequence data processing and analysis has been completed on the first 10 samples and is in progress for the subsequent samples. Alterations were detected in genes previously described to be affected in angiosarcoma. Recurrent mutations in TP53 were detected in 50% (5/10) of analyzed samples, comprising 3 missense mutations, 1 frameshift deletion, and 1 frameshift insertion. Alterations were seen in at least one sample in all other genes selected for this initial analysis. This initiative demonstrates the feasibility of studying tissues from geographically dispersed patients and serves as proof of concept that patient-driven genomics efforts can democratize research for exceedingly rare cancers. Enrollment is still in progress, and additional samples will be sequenced and analyzed at scale. The data generated from these studies will be deposited into the public domain in six-month intervals. Citation Format: Michael Dunphy, Esha Jain, Elana Anastasio, Mary McGillicuddy, Rachel Stoddard, Beena Thomas, Sara Balch, Kristin Anderka, Katie Larkin, Niall Lennon, Yen-Lin Chen, Andrew Zimmer, Esme O. Baker, Simone Maiwald, Jen Hendrey Lapan, Jason Hornick, Chandrajit Raut, George Demetri, Eric Lander, Todd Golub, Nikhil Wagle, Corrie Painter. The Angiosarcoma Project: Generating the genomic landscape of an exceedingly rare cancer through a nationwide patient-driven initiative [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5384.

The Metastatic Breast Cancer Project (MBCproject) is a research study that directly engages patients (pts) through social media and advocacy groups, and empowers them to share samples, clinical data, and experiences. The goal is to create a publicly available database of genomic, molecular, clinical, and patient-reported data to enable research. Working with pts and advocates, a website (MBCproject.org) was developed that allows pts with metastatic breast cancer (MBC) to register. Registered pts are sent an online consent form that asks for permission to obtain and analyze their medical records and samples. Once enrolled, pts are sent a saliva kit and asked to mail back a saliva sample, which is used to extract germline DNA. We contact participants' medical providers and obtain medical records and a portion of their stored tumor biopsies. Pts may be asked to mail in a blood sample, which is used to extract cell free DNA (cfDNA). Whole-exome sequencing (WES) is performed on tumor DNA, germline DNA, and cfNDA; transcriptome sequencing is performed on tumor RNA. Clinically annotated genomic data are used to study specific pt cohorts (including outliers) and to identify mechanisms of response and resistance to therapies. All de-identified data are shared via public databases. Study updates are shared with participants regularly. From 10/2015-11/2017, 4237 MBC pts registered, representing over 1,000 institutions. 95% answered the 16-question survey about their cancer, treatments, and demographic information. 2471 (58%) completed the consent form. 2,136 saliva kits were mailed to pts and 1,523 saliva samples were sent in (71%). 408 blood kits were mailed to pts and 175 blood samples have been received for cfDNA analysis. To date, we have obtained medical records from 311 pts and 190 tumors from 127 pts. In 10/2017, all data generated so far were publicly released on cbioportal.org, including WES for 103 tumors from 78 pts linked to clinical data including pathology (22 elements), medical record abstraction including all treatments and timelines/durations (67 elements), and patient-reported data (11 elements). 81% of biopsies included in this release were from the breast and 19% from metastatic sites. 75% were obtained prior to any therapy, 24% following therapy. New data will be released 4/2018 and every six months thereafter, as they are generated. Additional patient-reported data, including treatments, side effects, quality of life, family history, pregnancies, and sites of metastasis, will also be collected and shared. In summary, a patient-driven approach enabled rapid identification of thousands of MBC pts willing to share samples and clinical data. Remote acquisition of medical records, saliva, blood, and tumor tissue for pts across the U.S. is feasible. This shared clinico-genomic database should enable research in MBC and may serve as a model for patient-driven research in other cancers. Citation Format: Nikhil Wagle, Corrie Painter, Elana Anastasio, Michael Dunphy, Mary McGillicuddy, Rachel Stoddard, Esha Jain, Dewey Kim, Simona Di Lascio, Brett N. Tompson, Sara Balch, Beena Thomas, Priti Kumari, Shawn Johnson, Jamie Holloway, Ofir Cohen, Erik H. Knelson, Katie Larkin, Sam Pollock, Alicia Wong, Samira Bahl, Simone Maiwald, Andrew Zimmer, Esme O. Baker, Jen Hendry Lapan, Scott Sutherland, Scott Sassone, Viktor Adalsteinsson, Eric S. Lander, Todd R. Golub. The Metastatic Breast Cancer Project: Partnering with patients to accelerate progress in cancer research [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5371.

Summary. Numerous studies have described regulatory factors and sequences that control transcriptional responses in vitro. However, there is a paucity of information on the qualitative and quantitative regulation of heterologous promoters using transgenic strategies. In order to investigate the physiological regulation of human plasminogen activator inhibitor type-1 (hPAI-1) expression in vivo compared to murine PAI-1 (mPAI-1) and to test the physiological relevance of regulatory mechanisms described in vitro, we generated transgenic mice expressing enhanced green fluorescent protein (EGFP) driven by the proximal −2.9 kb of the hPAI-1 promoter. Transgenic animals were treated with Ang II, TGF-β1 and lipopolysaccharide (LPS) to compare the relative activation of the human and murine PAI-1 promoters. Ang II increased EGFP expression most effectively in brain, kidney and spleen, while mPAI-1 expression was quantitatively enhanced most prominently in heart and spleen. TGF-β1 failed to induce activation of the hPAI-1 promoter but potently stimulated mPAI-1 in kidney and spleen. LPS administration triggered robust expression of mPAI-1 in liver, kidney, pancreas, spleen and lung, while EGFP was induced only modestly in heart and kidney. These results indicate that the transcriptional response of the endogenous mPAI-1 promoter varies widely in terms of location and magnitude of response to specific stimuli. Moreover, the physiological regulation of PAI-1 expression likely involves a complex interaction of transcription factors and DNA sequences that are not adequately replicated by in vitro functional studies focused on the proximal −2.9 kb promoter.

ACE inhibition reduces plasminogen activator inhibitor-1 (PAI-1), a risk factor for myocardial infarction, whereas the effect of angiotensin receptor antagonism on PAI-1 is uncertain. The present study compares the time course of effects of ACE inhibition and angiotensin type 1 (AT 1 ) receptor antagonism on morning plasma PAI-1 antigen. Blood pressure and endocrine, metabolic, and fibrinolytic variables were measured in 20 insulin-resistant (defined by fasting glucose >8.3 mmol/L, body mass index >28 kg/m 2 , or fasting serum triglyceride ≥2.8 mmol/L) hypertensive subjects (mean age, 47.9±2.1 years) (1) before and after 1 week of hydrochlorothiazide 12.5 mg/d, and (2) before and 1, 3, 4, and 6 weeks after addition of ramipril (escalated to 10 mg/d) or losartan (escalated to 100 mg/d). Hydrochlorothiazide decreased systolic ( P =0.011) and diastolic ( P =0.019) pressure. Ramipril (from 133.6±5.1/94.5±2.4 to 127.0±3.1/91.4±3.3 mm Hg) or losartan (from 137.0±3.9/93.1±2.9 to 123.7±2.6/86.4±2.1 mm Hg) further reduced systolic ( P =0.009) and diastolic ( P =0.037) pressure. The pressure effects of the 2 drugs were similar. Hydrochlorothiazide increased plasma PAI-1 ( P =0.013) but not tissue-type plasminogen activator (tPA) ( P =0.431) antigen. Addition of either ramipril or losartan significantly decreased plasma PAI-1 antigen ( P =0.046). However, the effect of losartan on PAI-1 antigen was not sustained throughout the 6-week treatment period, such that there was a significant drug×time interaction ( P =0.043). tPA antigen decreased during either ramipril or losartan ( P =0.032), but tPA activity decreased only during losartan ( P =0.018). Short-term interruption of the renin-angiotensin-aldosterone system by either ACE inhibition or AT 1 receptor antagonism decreases PAI-1 antigen, but the duration of this effect is greater for ACE inhibition than for AT 1 receptor antagonism.

Antigen presentation by class II MHC proteins (MHC-II) is a critical component of the adaptive immune response to foreign pathogens. Our understanding of how antigens are presented has been greatly enhanced by crystallographic studies of MHC-II-peptide complexes, which have shown a canonical extended conformation of peptide antigens within the peptide-binding domain of MHC-II. However, a detailed understanding of the peptide loading process, which is mediated by the accessory molecule HLA-DM (DM), remains unresolved. MHC-II proteins appear to undergo conformational changes during the peptide loading/exchange process that have not been clearly described in a structural context. In the absence of a crystal structure for the DM-MHC-II complex, mutational studies have provided a low resolution understanding as to how these molecules interact. This review will focus on structural and biochemical studies of the MHC-II-peptide interaction, and on studies of the DM-MHC-II interaction, with an emphasis on identifying structural features important for the mechanism of DM mediated peptide catalysis.

HLA-DM is required for efficient peptide exchange on class II MHC molecules, but its mechanism of action is controversial. We trapped an intermediate state of class II MHC HLA-DR1 by substitution of αF54, resulting in a protein with increased HLA-DM binding affinity, weakened MHC-peptide hydrogen bonding as measured by hydrogen-deuterium exchange mass spectrometry, and increased susceptibility to DM-mediated peptide exchange. Structural analysis revealed a set of concerted conformational alterations at the N-terminal end of the peptide-binding site. These results suggest that interaction with HLA-DM is driven by a conformational change of the MHC II protein in the region of the α-subunit 3 10 helix and adjacent extended strand region, and provide a model for the mechanism of DM-mediated peptide exchange.

Background — Plasminogen activator inhibitor-1 (PAI-1) regulates fibrinolysis and has been reported to be an independent risk factor for ischemic cardiovascular events. This study describes the age-dependent development of spontaneous coronary arterial thrombi that are associated with evidence of subendocardial myocardial infarction in mice transgenic for human PAI-1. Methods and Results — We generated two independent transgenic mice founder lines that express a stable variant of active human PAI-1 under control of the murine preproendothelin-1 (mPPET-1) promoter. Backcrossed homozygous transgenic animals from founder line I had plasma PAI-1 levels of 23±12 ng/mL. PAI-1 transgenic animals younger than 4 months do not exhibit any evidence of arterial or venous thrombosis. Ninety percent of transgenic animals (n=10) older than 6 months developed spontaneous occlusions of typically multiple, penetrating coronary arteries, with histological evidence of subendocardial infarction identified in 50% of animals. Conclusions — This study shows that chronically elevated levels of PAI-1 are associated with age-dependent coronary arterial thrombosis in mice transgenic for human PAI-1. This is the first study of a murine model of coronary thrombosis that occurs in the absence of severe hypercholesterolemia or multiple genetic manipulations. These findings provide new evidence to support the hypothesis that PAI-1 excess contributes to the development of coronary arterial thrombosis.

Previous studies indicate that the vasodilator response to bradykinin (BK) and other endothelium-dependent and -independent agonists is decreased in black Americans compared with white Americans. The purpose of the present study was to determine the effect of ethnicity on fibrinolytic function in humans. Graded doses of BK (100, 200, and 400 ng/min), acetylcholine (15, 30, and 60 μg/min; N=20), or methacholine (3.2, 6.4, 12.8 μg/min; N=20), and sodium nitroprusside (0.8, 1.6, and 3.2 μg/min) were infused via brachial artery in 19 white and 21 black age-matched normotensive subjects. Forearm blood flow (FBF) was measured by plethysmography, and venous and arterial samples were collected for tissue plasminogen activator (tPA) antigen. Compared with whites (increase in FBF from 3.7±0.5 to 23.9±2.5 mL · min −1 · 100 mL −1 ), blacks (increase in FBF from 2.8±0.3 to 15.2±1.9 mL · 100 mL −1 · min −1 ) exhibited a blunted FBF response to BK ( P =0.035). Responses to sodium nitroprusside and methacholine or acetylcholine were similarly decreased. In contrast, there was no effect of ethnicity on net tPA antigen release in response to BK (increase from −0.2±0.4 to 67.3±15.2 ng · min −1 · 100 mL −1 in blacks; from 0.04±0.9 to 65.9±13.6 ng · min −1 · 100 mL −1 in whites). Thus, ethnicity significantly influenced the relationship between the flow and tPA release responses to BK ( P =0.037). These data suggest that the BK-dependent alterations in vascular fibrinolytic function are preserved in black Americans compared with white Americans.

The recent success of the anti-CLTA-4 antibody, ipilimumab, for late stage metastatic melanoma, provides proof of principle that stimulating the immune system can have profound effects on patient outcome. However, a detailed understanding of the role of immune-modulating cells within the tumor microenvironment has been confounded by the lack of a suitable model system that would allow for direct visualization of cells within the intact tumor microenvironment. Previous work has demonstrated that the zebrafish, Danio Rerio, can be genetically manipulated to produce melanomas that recapitulate BRAFV600E;P53-/- human tumors. Due to its translucency, ease of genetic manipulation and high fecundity, the zebrafish is an attractive model system that allows for in vivo characterization of cells within intact tissue. Using this model system, we have begun investigating the adaptive immune response to melanoma in zebrafish. We have focused our initial investigations on determining whether transcript expression of key adaptive immune-modulatory proteins are present in the zebrafish and to what extent they are expressed intratumorally . Our studies have found that orthologs of CLTA-4, FOXP3, and CD8 are all expressed in wild-type zebrafish, but not in rag-/- zebrafish. Furthermore, transcript levels of CTLA-4 were greatest in the melanoma tumor relative to other regions of the zebrafish, which is consistent with the constitutive expression of CTLA-4 in human melanomas. Additionally, we have cloned the promoters for zebrafish FOXP3 and CD8 and are developing fluorescent reporter lines that will enable us to visualize and ablate subpopulations of T cells within the tumor. These lines, along with previously described reporter lines for MHC II and lck, will enable us to determine the role of adaptive immune cells during melanoma onset and progression in the zebrafish. Our research supports the notion that there is conservation between the human and zebrafish adaptive immune systems, and that similar immune evasion mechanisms may be contributing to melanoma growth in zebrafish. These data position the zebrafsh as a powerful model system for immunological investigations that focus on the adaptive immune response to melanoma. Citation Format: Corrie A. Painter, Craig Ceol. Adaptive immunity in a zebrafish model of melanoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1273. doi:10.1158/1538-7445.AM2013-1273

Background Major histocompatibility complex proteins are believed to undergo significant conformational changes concomitant with peptide binding, but structural characterization of these changes has remained elusive. Methodology/Principal Findings Here we use molecular dynamics simulations and experimental probes of protein conformation to investigate the peptide-free state of class II MHC proteins. Upon computational removal of the bound peptide from HLA-DR1-peptide complex, the α50-59 region folded into the P1-P4 region of the peptide binding site, adopting the same conformation as a bound peptide. Strikingly, the structure of the hydrophobic P1 pocket is maintained by engagement of the side chain of Phe α54. In addition, conserved hydrogen bonds observed in crystal structures between the peptide backbone and numerous MHC side chains are maintained between the α51-55 region and the rest of the molecule. The model for the peptide-free conformation was evaluated using conformationally-sensitive antibody and superantigen probes predicted to show no change, moderate change, or dramatic changes in their interaction with peptide-free DR1 and peptide-loaded DR1. The binding observed for these probes is in agreement with the movements predicted by the model. Conclusion/Significance This work presents a molecular model for peptide-free class II MHC proteins that can help to interpret the conformational changes known to occur within the protein during peptide binding and release, and can provide insight into possible mechanisms for DM action.